Data from: USP37 prevents premature disassembly of stressed replisomes by TRAIP
Data files
Jun 25, 2025 version files 9.42 MB
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Fig1A_drugZ_result.xlsx
1.08 MB
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Fig1A_guide_counts.tsv
2.74 MB
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Fig2A_drugZ_result.xlsx
2 MB
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Fig2A_guide_counts.tsv
3.59 MB
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README.md
2.46 KB
Abstract
The E3 ubiquitin ligase TRAIP associates with the replisome and helps this molecular machine deal with replication stress. While TRAIP promotes DNA inter-strand crosslink repair by triggering the disassembly of CDC45-MCM2-7-GINS (CMG) helicases that have converged on these lesions, disassembly of single CMGs that have stalled temporarily would be deleterious, suggesting that TRAIP must be carefully regulated. Here, we demonstrate that human cells lacking the de-ubiquitylating enzyme USP37 are hypersensitive to topoisomerase poisons and other replication stress-inducing agents. We further show that TRAIP loss rescues the hypersensitivity of USP37 knockout cells to topoisomerase inhibitors. In Xenopus egg extracts depleted of USP37, TRAIP promotes premature CMG ubiquitylation and disassembly when replisomes stall before they have fully converged. Finally, we provide evidence that USP37 binds replisomes via CDC45, and that this interaction mediates USP37’s response to topological stress. Based on these results, we propose that USP37 protects genome stability by preventing TRAIP-dependent CMG unloading when replication stress impedes timely termination.
https://doi.org/10.5061/dryad.34tmpg4tn
Description of the data and file structure
Counts and analyses of CRISPR screens.
Suffixes indicate the type of data:
- Fig*****_drugz_result.xlsx – Results from analyses using DrugZ. Comparisons were of DMSO vs camptothecin treated cells of the same genotype. See DrugZ paper for details of the algorithm and precise definitions of the statistics reported (https://doi.org/10.1186/s13073-019-0665-3). Columns defined below:
- GENE: Gene symbol, as used in the counts files.
- sumZ: Un-normalised summed Z-scores per gene.
- numObs: Number of observations (guides) per gene.
- normZ: Normalised summed Z-score.
- pval_synth: p-value of synthetic lethality (i.e. the combination of guides targeting the named gene and the treatment caused decreased abundance).
- rank_synth: Rank when ordered by most synthetically lethal.
- fdr_synth: False discovery rate corrected significance of pval_synth.
- pval_supp: p-value of synthetic viability (the opposite of synthetic lethality).
- rank_supp: Rank when ordered by most synthetically viable.
- fdr_supp: False discovery rate corrected significance of pval_supp.
- Fig***_guide_counts.tsv** – CRISPR guide abundances
- The first two columns ("guide" and "gene") give CRISPR guide id and gene symbol for each row. Subsequent columns are guide abundances for the named sample.
- sample details:
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Replicate Treatment Background WT-Essentialome_S4 Essentialome WT WT-Initial Initial WT USP37KO-Clone17-Essentialome_S9 Essentialome USP37KO USP37KO-Clone6-Essentialome_S5 Essentialome USP37KO USP37KO-Initial-B2_S1 Initial USP37KO USP37KO-Initial-B1_S1 Initial USP37KO WT2-CTRL_S5 CONTROL WT WT-CTRL_S1 CONTROL WT WT-CPT_S2 Camptothecin WT WT2-CPT_S6 Camptothecin WT
For CRISPR/Cas9 screens, biological duplicates of U2OS Cas9 wild-type and USP37 KO cells were transduced at a MOI of 0.3 and 500-fold coverage of the Brunello library (Doench et al., 2016). Afterward, transductants were selected with 1.5 µg/mL puromycin for 12 days. Library preparation and next-generation sequencing of the samples was performed as described previously (Bowden et al., 2020). Guide-enrichment analysis was performed using DrugZ (Colic et al., 2019).